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Mayor Thomas M. Menino surged to the top of the field and Councilor at Large Michael F. Flaherty Jr. grabbed second place in Boston’s preliminary mayoral race yesterday, setting up a general election that pits two former allies who have become sharp political adversaries.

Menino captured 50.5 percent of the vote, while Flaherty got 24 percent, beating out the other challengers by a comparatively slim margin for a spot in the final election. Councilor at Large Sam Yoon ended the day with 21 percent, and South End businessman Kevin McCrea got 4 percent.

In their victory speeches, Menino and Flaherty displayed dramatically different postures, potentially foreshadowing a fierce six-week campaign that will culminate with the Nov. 3 election.

“We’re going to engage in a positive campaign, about the future of the city,’’ Menino told scores of supporters at his election night party at the unadorned headquarters of the International Brotherhood of Electrical Workers Local 103 in Dorchester. “Come join us. Together, we will continue to move Boston forward.’’

Flaherty, speaking to a room packed with backers at a Dorchester restaurant, signaled he plans to go after Menino aggressively. He said the city cannot wait another four years for new leadership and led the crowd in a chant of “We can’t wait! We can’t wait!’’

“If everyone in this room stands with me and rolls up your sleeves and throws a shoulder into this effort, we will change Boston,’’ he said.

Yesterday’s contest marked the end of the first chapter in Menino’s toughest battle for reelection since he took office 16 years ago. Already the longest serving mayor in city history, he is seeking a fifth 4-year term.

Also yesterday, a wide field of council candidates vied for eight places in the general election. Incumbent councilors John R. Connolly and Stephen J. Murphy made the ballot, as did Felix G. Arroyo, Ayanna Pressley, Andrew Kenneally, Tito Jackson, Doug Bennett, and Tomas Gonzalez. In a notable development, Councilor Chuck Turner, under federal indictment on corruption charges, easily topped his race with nearly 53 percent of the vote in his district.

At Yoon’s election night gathering at a Masonic social hall in Dorchester, an energized, diverse, and mostly young crowd of about 200 was expectant, upbeat, but realistic that their candidate faced a hard road yesterday.

“I want you all to know that there is nothing I regret about doing this,’’ Yoon told his supporters. ’’And there is nothing you should regret one iota.’’

Over at Wally’s Cafe Jazz Club, a storied bar in the South End where “Let the Good Times Roll’’ played on a neon jukebox, a smattering of McCrea supporters watched results coming in on the lone television. McCrea, wearing a campaign button, said he was happy with the day’s turnout.

“I’m feeling fantastic,’’ he said in an interview. “People across the city today were thanking me for being in the race.’’

Interviews with voters across the city yesterday found that the dominant issue in the campaign was not schools or public safety or property taxes, but the mayor. Many who voted for Flaherty, Yoon, and McCrea said they were casting ballots not necessarily for one of those candidates, but against the status quo.

In West Roxbury, Jim Ryan, 70, a former newspaper pressman and shop owner, said he voted for Flaherty because “Menino’s been in there long enough.’’ In Jamaica Plain, teacher Joe Golding, 35, voted for Yoon “to see new and different plans in Boston.’’ In Roxbury, Omar Franklin, 48, an associate minister, cast his ballot for Flaherty because, “we need change.’’

Still, thousands of voters stood by the longtime mayor, gushing about his record, his personal touch, and his leadership style.

In the South End, Suezanne Bruce, 27, said she cast her ballot for Menino because “if it’s not broke, don’t fix it.’’ In Roxbury, 83-year-old Thelma Henderson voted for Menino because “that’s my man, he looks out for me.’’ In Charlestown, homemaker Patricia Murphy, 64, said Menino must be a good mayor to still be in office.

“If he was a bad person, he would have been voted out a long time ago,’’ she said, “because the voters are not foolish.’’

The race energized more voters than in any mayoral preliminary since Menino took office, with 81,641 residents casting ballots. That was nearly double the number who voted in each of the last two preliminary elections, in 2005 and 2001.

The highest turnouts were in South Boston and West Roxbury, both hotly contested battlegrounds. South Boston, Flaherty’s home neighborhood, had logged more than 7,500 voters. In West Roxbury, home to many city employees who have supported Menino, and firefighters, who are backing Flaherty, nearly 9,400 residents voted.

The competitive mayor’s race, and an unusually large, 15-person field vying for at-large seats on the City Council, made for a lively day of voting and last-minute campaigning.

Outside Holy Name Parish Hall in West Roxbury, traditionally one of the busiest polling stations in Boston, Menino stopped by in the morning, and Flaherty greeted voters in the afternoon and evening.

A GMC Sierra plastered with Flaherty signs and featuring a license plate spelling “GOTV,’’ get out the vote, was driving in circles around a nearby rotary while blaring messages such as “it’s time for a change!’’ from a rooftop loudspeaker. A Teamsters van plastered with Menino signs was parked in the Holy Name lot.

One 81-year-old West Roxbury voter said the battle outside mirrored his internal struggle, which also was “more or less a conflict between Menino and Flaherty.’’ But the retired clerical worker, Richard Fallona, said he ended up voting for Menino.

“He’s kept at it,’’ said Fallona, wheeling a shopping cart as he stopped by to vote on his way to the grocery store. “He’s kept Boston moving.’’

But another voter, Brendan Adams, 36, who works in the schools, opted for Flaherty.

“The Boston public schools - they’re a mess,’’ he said. “We need new leadership. We need someone who’s actually going to be sitting behind the desk, not just cutting ribbons all day.’’

Across the city in South Boston, also a traditionally voter-rich area, the choice for many also appeared to be between Menino and Flaherty. Adrienne Callaghan, 27, said she threw her support behind Flaherty because he brings “new ways to look at old problems.’’

“And I tend to not like change,’’ she said. “I’ve grown up with Mayor Menino in office my whole life.’’

At the same polling place, Karen Cahill said she blackened the oval next to the name of the longtime mayor. “He’s done a lot of things that people overlook,’’ Cahill said, explaining that her support of the four-term incumbent never wavered. “He’s done a lot for parks. He’s done a lot for services.’’

Many who voted for Menino said they had met him or had been touched personally by his administration.

Henderson, the 83-year-old Roxbury resident, said the Menino administration has called her and stopped by her house during the sweltering days of summer. “He made sure I was comfortable during the hot days,’’ she said.

Some voters said they were undecided yesterday. At Morning Star Baptist Church in Mattapan, Reginald Phillips, 32, said he left the box for mayor blank on his ballot. Phillips said that he was leaning toward Yoon, but he was not sure of the candidate’s stance on various issues, such as crime and poverty. He said Menino has talked about more jobs and affordable housing, but he has not seen it. And he said he basically does not trust Flaherty.

“I was thinking about it for weeks, and I usually just pick someone,’’ he said. “But this time I couldn’t make up my mind.’’